Research workbench
X-ray structure of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5- phosphate reductase
Analyse X-ray structure of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5- phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AZN
- Type
- protein
- Length
- 1,314 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative 5-amino-6-(5-PHOSPHORIBOSYLAMINO)URACIL reductase
- EC
- 1.1.1.193
- UniProt
- Q58085
- Ligands
- MA5, NAP
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Putative 5-amino-6-(5-PHOSPHORIBOSYLAMINO)URACIL reductase (EC 1.1.1.193) | protein | 219 | 26% helix, 27% strand | Q58085 |
Ligands and binding sites
- MA5 · 2-(6-(2-cyclohexylethoxy)-tetrahydro-4,5-dihydroxy-2(hydroxymethyl)-2H-pyran-3-yloxy)-tetrahydro-6(hydroxymethyl)-2H-py ran-3,4,5-triol · ligand · 8 copies · chains A, C, B, D, E, F
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.72 | 0.80 | 52 | NAP |
| 2 | 622 | 0.72 | 0.80 | 51 | NAP |
| 3 | 587 | 0.72 | 0.80 | 50 | NAP |
| 4 | 580 | 0.72 | 0.80 | 53 | NAP |
| 5 | 593 | 0.72 | 0.80 | 54 | NAP |
Interfaces
7 interfaces between chains.
- A–D · 471 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 354 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 353 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 331 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 327 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 2AZN · X-RAY Structure of 2,5-diamino-6-ribosylamino-4(3h)-pyrimidi 5-phosphate reductase · the same entry in another collection · chain C against C, TM-score 1.00
- Q58085 · AlphaFold monomer V2.0 prediction for 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone… · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q58085
- Elsewhere: RCSB PDB 2AZN · PDBe 2AZN · UniProt Q58085
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